Subnational analysis of the COVID-19 epidemic in Brazil

Brazil is currently reporting the second highest number of COVID-19 deaths in the world. Here we characterise the initial dynamics of COVID-19 across the country and assess the impact of non-pharmaceutical interventions (NPIs) that were implemented using a semi-mechanistic Bayesian hierarchical modelling approach. Our results highlight the significant impact these NPIs had across states, reducing an average Rt > 3 to an average of 1.5 by 9-May-2020, but that these interventions failed to reduce Rt < 1, congruent with the worsening epidemic Brazil has experienced since. We identify extensive heterogeneity in the epidemic trajectory across Brazil, with the estimated number of days to reach 0.1% of the state population infected since the first nationally recorded case ranging from 20 days in São Paulo compared to 60 days in Goiás, underscoring the importance of sub-national analyses in understanding asynchronous state-level epidemics underlying the national spread and burden of COVID-19. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work used the Cirrus UK National Tier-2 HPC Service at EPCC ([http://www.cirrus.ac.uk][1]) funded by the University of Edinburgh and EPSRC (EP/P020267/1). We would like to thank Amazon AWS and Microsoft Azure for computational credits. We would like to thank the Stan Development team for their constant support. We acknowledge the Medical Research Council and FAPESP (MR/S0195/1). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study is based on data available in the public domain. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data and code used is publicly available. [1]: https://www.cirrus.ac.uk